Tag: GIAB

 As Marvel superheroes traverse the multiverse to save the day, genomics researchers are our superheroes as they navigate the daunting multiverse that is biology. The complex and dynamic interactions between the genome sequence, its epigenetic regulation, and their combined effects on transcript expression and splicing are fundamental to our understanding…

Homozygous reference genotype for a GIAB genome 0 GIAB VCFs (v4.2.1) provides 0/1, 1/0 (ALT-heterozygous) & 1/1 (ALT- homozygous) genotypes (in addition 1/2, 2/1, & 2/2 where there are more than one ALT alleles). GIAB also provides a BED file where any other position not in the VCF can be…

What was once the final frontier of the human genome — the Y chromosome — has just been mapped out in its entirety. Led by the National Human Genome Research Institute (NHGRI), a team of researchers at the National Institute of Standards and Technology (NIST) and many other organizations used…

Summary: Researchers successfully sequenced the entire Y chromosome, previously considered the most elusive part of the human genome. This feat enhances DNA sequencing accuracy for this chromosome, aiding the identification of genetic disorders. Using state-of-the-art technologies, the team pieced together over 62 million letters of genetic code. This breakthrough, in…

Skaletsky, H. et al. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature 423, 825–837 (2003). Article  ADS  CAS  PubMed  Google Scholar  Miga, K. H. et al. Centromere reference models for human chromosomes X and Y satellite arrays. Genome Res. 24, 697–707 (2014)….

Can I say variant called from GIAB confidence region from any sample is real? 1 Hi all, I have a question about GIAB confidence region! I know it is normally used for benchmarking. But when people do variant calling from their sample. Is it ok to say that variant called…

PacBio Pipeline and Tools for Variant Call 0 Hi, I am new to long read seq, I am trying to call Variants on GIAB Trio samples from PacBio data Initially i Aligned reads with Pbmm2 tool, then variant call by DeepVariant 1.5, Phasing through Whatshap. My queries are as follows…

Edit and re-head BAM file 0 Hi there I have a BAM file which needs to be edited and re-headed. Now, I’m aware of how to do so the problem is that for some reason the sed command I’m using does not catch the sequence I have to remove… Below,…

Ethical approval, DNA samples and oligonucleotides All patients provided written informed consent to allow the collection of blood and/or tumor tissue and the analysis of clinical and genetic data for research purposes. The IRB of the Dana-Farber Cancer Institute and New York University Grossman School of Medicine approved these protocols….

Review doi: 10.1038/s41576-023-00590-0. Online ahead of print. Affiliations Expand Affiliations 1 Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA. 2 UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA. 3 Baylor College of Medicine, Human Genome Sequencing Center, Houston, TX, USA….

Does anyone know if there is a somatic truth set vcf available? I know there are now several available for germline samples from GIAB I read this paper Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection but it looks as though they don’t provide the actual vcf…

Hi, Does anyone know what coverage the GIAB truth set is for NA12878? I was wanting to download the vcf from here [GIAB truthset vcf ][1]but it would be good to know what the mean coverage is. I have read this paper [Best practices for benchmarking germline small-variant calls in…

NEW YORK – During beta testing for Element Biosciences’ new sequencer last year, one of the customers quickly ran into a problem when trying it out with 10x Genomics’ single-cell assays. 10x’s Cell Ranger software, used for single-cell sequencing data analysis, was aborting runs and spitting out error messages. The reason?…

Introduction The reduced cost of DNA sequencing technology has led to an exponential growth of raw sequencing data. To keep pace with this development, secondary analysis tools that can provide fast and accurate results in a cost-effective manner are needed to extract actionable genomic insights. Illumina’s DRAGENTM (Dynamic Read Analysis for GENomics) addresses…

GIAB and GRCh38 SV/CNV 1 Does anyone know the release status of gold standard datasets SV/CNV for GRCh38 in GIAB? I see a “Preliminary results of T2T benchmark” – which is wonderful – but then, I’d expect GRCh38 data to be already available, is it? Can’t find it… benchmarking •…

Hello, I am trying to learn DNA sequencing analysis by using GIAB datasets [Link to Chinese trio – HG005_NA24631_son/], the readme file they had provided does not provide the adapter sequences used. I tried to use bbmerge.sh like in this biostars post ; bbmerge.sh in1=r1.fq in2=r2.fq outa=adapters.fa and it identified…

This blog post was contributed by Don Freed, Senior Bioinformatics Scientist, and Brendan Gallagher, Head of Business Development at Sentieon; and Olivia Choudhury, PhD, Senior Partner Solutions Architect, Sujaya Srinivasan, Genomics Solutions Architect, and Aniket Deshpande, Senior Specialist, HPC HCLS at AWS. The year 2022 was an exciting one for genomics…

Sample preparation We ordered the GIAB samples from the Coriell Institute (NA24385, NIST ID HG002; NA24149, NIST-ID HG003 and NA24143, NIST-ID HG004). DNA concentration was measured by Qubit. The library was constructed according to Illumina TruSeq DNA PCR Free Library Prep protocol HT (Illumina Inc., San Diego, CA, USA) for…

Sequencing data We used publicly available sequencing data from the GIAB consortium45, 1000 Genomes Project high-coverage data46 and Human Genome Structural Variation Consortium (HGSVC)4. All datasets include only samples consented for public dissemination of the full genomes. Statistics and reproducibility For generating the assemblies, we used all 14 samples for…

Abstract Despite the tremendous increase in omics data generated by modern sequencing technologies, their analysis can be tricky and often requires substantial expertise in bioinformatics. To address this concern, we have developed a user-friendly pipeline to analyze (cancer) genomic data that takes in raw sequencing data (FASTQ format) as input…

GIAB Benchmark (High Confidence) Bed Filles 0 Hi all, I havent used Genome in a Bottle for a couple of years. When I did use it, I recall I would download samples in VCF format for: AshkenaziTrio (three each) NA12878 (only one) ChineseTrio (three each) I would then download what…

qualimap2 mean mapping quality 0 I’ve done a contrast experiment to see the difference between the bam with BQSR and the bam without BQSR. I use qualimap to evaluate both bams. This is the confusing part. Using hap.py and the giab na12878 truth vcf, shows the bam with BQSR is…